Yevamos 42a - Waiting 3 Months after Conversion

A Jewish man lived with a non-jewish woman for years, she then converted and he did teshuvah, do they have to wait 3 months before getting married?

First, the mishnah 24b says that a non-jewish women who is suspected of having relations with a jewish man cannot marry her after she converts. The reason given in the gemara (explained by rashi) is that getting married strengthens the suspicion that they did in fact have relations. However, R' Shlomo Kluger in Shulchan Aruch (E.H. 11:5) points out that if they definitely had relations (not just suspect), then it should be permitted since in that case the marriage is not strengthening the "rumors", since we know for sure that they were mezaneh. However, the Nimukei Yosef (brought in Beis Shmuel) says that even if they definitely had relations, they cannot get married. R' Moshe (Igros E.H. 1:27) is mechadesh that the Nimukei Yosef is concerned that by getting married they would be publicizing the sin that they commited by having relations. This only applies to a situation where we know for sure they had relations but it was not public knowledge, however when they actually lived together, so it is public knowledge, one is supposed to publicize the aviera when they do teshuva.

Regarding waiting 3 months, R' Moshe writes matter of factly that she must wait. I don't understand why she needs to wait. We require havchana whenever we don't know who the father is, or don't know if conception occurred before or after his conversion (either for the purpose of shechina resting, or for the purpose of not leading to ervah). But, here everything is very clear, the child is Jewish since she converted while pregnant (or before she became pregnant). The father was jewish the whole time so that any son born later will be a brother both from the father and from the mother, so there won't be any concern even if yibum is done. Why would there be a need for havchana?

Perhaps the need for havchana is bec. we are concerned that before she converted she had z'nus with someone else. This is really a machlokes on 35a whether a convert has to wait 3 months or do we assume that she avoided becoming pregnant since she had in mind to convert. Although the Beis Yosef (13:5) argues on the magid mishna and says that we are concerned that she was mezaneh and became pregnant, in Shulchan Aruch he seemed to come out that she does not have to wait (Beis Shmuel 13:7). Why then is R' Moshe machmir for havchana? Is there any point in havchana to determine whether conception occurred before or after she converted (it shouldn't make a difference for anything)?